Treatment of suspension cells of Ginkgo biloba with fungal endophytes resulted in accumulation of flavonoids, increased abscisic acid (ABA) production and activation of phenylalanine ammonia-lyase (PAL). Fluridone, an inhibitor of ABA biosynthesis, was effective in inhibiting fungal endophytes-induced ABA biosynthesis, increase of PAL activity and flavonoids accumulation. Moreover, exogenous application of ABA enhanced PAL activity and increased accumulation of flavonoids in G. biloba cells with or without fungal endophytes elicitor. These finding suggest a causal relationship between ABA release and both PAL activity and flavonoid accumulation under fungal endophytes treatment and that ABA is involved in fungal endophytes-induced flavonoids accumulation in this plant.